Two nucleotides were deleted near the 3' end of ORF DEP1/YAL013W, altering its coding sequence. The start and most of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 15 amino acids shorter.

Nucleotide changes within the coding region of DRS2/YAL026C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residues 45-46 are now AN rather than GY, residue 450 is now Alanine rather than Arginine, residue 674 is now Proline rather than Glycine, residues 891-892 are now NT rather than KS, residues 953-954 are now GD rather than AS, and residue 987 is now Valine rather than Leucine.

The following changes were made to the systematic sequence of Chromosome I in the region encompassing features FLO9/YAL063C and GDH3/YAL062W: deletion of the A at 29254, deletion of AAT at 29289-29291, transversion of T to A at 29301, and deletion of the A at 29307.

Kellis et al. 2003 predicted and confirmed the deletion of a single G nucleotide at chromosomal coordinate 166772. As a consequence of this sequence change, YAR014C was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 702 to 707 amino acids.

Nucleotide changes within the coding region of CDC15/YAR019C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 316 is now Alanine rather than Arginine, residue 321 is now Alanine rather than Proline, and 900-902 are now KDV rather than NGC.

The work of Kellis et al. 2003 predicted the deletion of 2 separate G nucleotides in YAL051W at chromosomal coordinates 51688 and 51694, and these sequence errors were confirmed in S288C by SGD. As a consequence of these changes, YAL051W was shortened at the 3' end, altering the C-terminus and decreasing the size of the predicted protein from 1062 to 1047 amino acids.

The following changes were made to the systematic sequence of Chromosome I in the region encompassing features YARCdelta8 and YAR060C: deletion of the T at 210804, transversion of T to A at 210810, and transition of C to T at 211011.

A single C nucleotide was inserted very near the 3' end of ORF YAR019W-A, altering its coding sequence. The start and most of the reading frame remain the same, but the C-terminus has changed and the annotated protein is now 4 amino acids shorter.

Kellis et al. 2003 and Cliften et al. 2003 predicted and confirmed the insertion of a single C nucleotide after the C at chromosomal coordinate 143848. As a consequence of this sequence change, YAL002W was extended at the 5' end, altering the N-terminus and increasing the size of the predicted protein from 1176 to 1274 amino acids.

Kellis et al. 2003 and Brachat et al. 2003 predicted and confirmed the insertion of a single C nucleotide after the C at position 130239 on Chromosome I. As a consequence of this sequence change, YAL013W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein from 362 to 420 amino acids. They also found an additional seqeuncing error: the CG at 130246-130247 should be GC.

Due to the insertion of a single T nucleotide after the T at coordinate 128441 in the systematic sequence of Chromosome I, the ORF SUN8/YAL014C was extended 450 nucleotides in the 3' direction, making the protein product 150 amino acids longer at the C-terminus. Thanks to Lena Burri, Trevor Lithgow, and Hugh Pelham for reporting this sequence error in the systematic sequence of SYN8/UIP2/YAL014C to SGD.

Due to the insertion of CC after the C at 108137, and the insertion of a G after the G at 108143 in the systematic sequence of Chromosome I, the coordinates of PMT2/YAL023C have been changed. Thanks to Verena Girrbach (verena.girrbach@biologie.uni-regensburg.de) for reporting this sequence error in the systematic sequence of PMT2/FUN25/YAL023C to SGD.

A single A nucleotide was inserted within ORF YAL064W, near its 5' end, moving the start codon out of frame with the rest of the protein. The C-terminus and majority of the reading frame remain the same, but the N-terminus has changed and the annotated protein is now 14 amino acids shorter.

Six separate single nucleotides were inserted within ORF BUD14/YAR014C, and three single nucleotide substitutions were also made, altering its coding sequence. The start, stop, and majority of the reading frame remain the same, but the annotated protein is now two amino acids longer and a small section of the protein sequence is now different.

Kellis et al. 2003 predicted and confirmed the insertion of a single G nucleotide after the T at chromosomal coordinate 41778. As a consequence of this sequence change, YAL056W was extended at the 3' end, altering the C-terminus and increasing the size of the predicted protein increasing from 847 to 880 amino acids.

Insertion of a single G after the G at 193300 merged SWH1/YAR042W and OSH1/YAR044W. After merging YAR042W (coordinates 192613-193383 (1-771)) and YAR044W (coordinates 193599-196178 (1-2580)), the coordinates of the merged ORF, SWH1/YAR042W, are 192613-196179 (1-3567). OSH1 and YAR044W are now aliases of SWH1/YAR042W. This sequence change was predicted by several studies, then verified in S288c by SGD.

Three single nucleotide substitutions were made within the coding
sequence of SSA1 (at nucleotide positions 623, 1252, and 1265 relative
to the SSA1 coding sequence), based on the sequence reported by Slater
and Craig (1989) and corresponding to GenBank entry X12926. These
changes result in phenylalanine to serine changes at amino acid
residues 208 and 422 and a change from serine to proline at amino acid
residue 418. Thanks to Andreas Bracher for bringing these corrections
to our attention.

Note that the change at position 623 of SSA1 also affects the
coding sequence of the Dubious ORF YAL004W.

A single nucleotide substitution within the coding region of MDM10/YAL010C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 272 is now Asparagine rather than Glutamine.

A single nucleotide substitution within the coding region of PSK1/YAL017W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 73 is now Glutamic Acid rather than Glutamine.

The substitution of two nucleotides within the coding region of ATS1/YAL020C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 305 is now Glycine rather than Alanine.

A single nucleotide substitution within the coding region of MAK16/YAL025C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 250 is now Glutamic Acid rather than Glutamine.

A single nucleotide substitution within the coding region of BDH1/YAL060W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 322 is now Aspartic Acid rather than Alanine.

Three single base substitutions were made within ORF YAL044C/GCV3 to correct errors in the systematic reference sequence for Chromosome I: Two separate A -> C transversions at 58196 and 58247, and a C -> T transition at 58424. These errors were verified by sequencing in 3 different strains, all of ResGen BY4741 (S288C) background. SGD thanks Michael E. Rice for bringing these errors to our attention, and for verifying the correct sequence.

Nucleotide changes within the coding region of SPC72/YAL047C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 302 is now Asparagine rather than Isoleucine.

Nucleotide changes within the coding region of OAF1/YAL051W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 70 is now Arginine rather than Tryptophan, residue 447 is now Glutamine rather than Proline, and residue 588 is now Lysine rather than Threonine.

Nucleotide changes within the coding region of FLC2/YAL053W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 111 is now Cysteine rather than Serine, residue 312 is now Asparagine rather than Aspartic Acid, and residues 641-643 are now NDS rather than IDP.

Nucleotide changes within the coding region of GPB2/YAL056W resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 661 is now Valine rather than Isoleucine, residue 802 is now Cysteine rather than Phenylalanine, and residues 814-815 are now ED rather than AA.

A single nucleotide substitution within the coding regions of overlapping ORFs ECM1/YAL059W and YAL059C-A resulted in altered protein sequences for both ORFs. The start, stop, and reading frames remain the same for both proteins, but ECM1/YAL059W protein residue 102 is now Alanine rather than Aspartic Acid, and YAL059C-A protein residue 36 is now Alanine rather than Serine.

The substitution of two nucleotides within the coding region of YAR023C resulted in an altered protein sequence. The start, stop, and reading frame remain the same, but protein residue 20 is now Phenylalanine rather than Valine, and residue 46 is now Phenylalanine rather than Isoleucine.

When confirming the G nucleotide insertion that resulted in the merger of SWH1/YAR042W and OSH1/YAR044W (see 2003-09-27), SGD detected an additional sequencing error. The substitution of an A nt for a G nt changes amino acid 248 from a serine to an asparagine.

As part of SGD's genome annotation revision R64.2, new ARS consensus sequences were annotated within the following ARS elements on Chromosome I based on Liachko et al. 2013: ARS104, ARS106, ARS107, ARS110, ARS111.

As part of SGD's genome annotation revision R64.2, the two pseudogenes YAR061W + YAR062W have been combined into a single pseudogene, keeping the name YAR061W. This region is homologous to parts of FLO1/YAR050W and FLO9/YAL063C, but contains stop codons at several positions.

This RNA gene, HRA1, was described by Samanta et al. (2006). Approximate start and stop coordinates, which are accurate to within 25 nucleotides, have been specified for this non-coding RNA. Many thanks to Manoj Samanta for alerting us to this noncoding RNA.

The previously annotated boundaries of CEN1 were adjusted to coincide with the 5' end of CDEI and the 3' end of CDEIII, to more accurately reflect current knowledge regarding centromere structure in Saccharomyces cerevisiae.

The start site of FUN19/YAL034C was moved 150 nt (50 codons) downstream, based on the automated comparison of closely-related Saccharomyces species by Kellis et al. 2003. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been updated. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

The start site of GCV3/YAL044C was moved 21 nt (7 codons) downstream, based on the automated comparison of closely-related Saccharomyces species by Kellis et al. 2003. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been updated. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

The start site of YAL011W was moved 39 nt (13 codons) downstream, based on the automated comparison of closely-related Saccharomyces species by Kellis et al. 2003. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been updated. Evidence supporting this change includes: 1) This is the predicted start methionine in the majority of Saccharomyces species orthologs analyzed by Kellis et al. and/or Cliften et al.; 2) Significant sequence conservation begins abruptly at this predicted start methionine.

The chromosomal locations for the following telomeric features on Chromosome I were generously provided by Ed Louis and Dave Barton (University of Leicester, UK): TEL01L, TEL01L-TR, TEL01L-XC, TEL01L-XR, TEL01R, TEL01R-TR, and TEL01R-XC.